31 votes
Accepted

Why do some assemblers require an odd-length kmer for the construction of de Bruijn graphs?

From the manual of Velvet: it must be an odd number, to avoid palindromes. If you put in an even number, Velvet will just decrement it and proceed. the palindromes in biology are defined as ...
Kamil S Jaron's user avatar
14 votes

Why do some assemblers require an odd-length kmer for the construction of de Bruijn graphs?

To expand on the answer above, in case it isn't clear, we show: Why palindromic sequences must be even in length Why palindromic sequences induce self-loops in a de Bruijn graph Why self loops in a ...
ukemi's user avatar
  • 243
7 votes

How to make a distinction between the "classical" de Bruijn graph and the one described in NGS papers?

Several papers have made this distinction, and a few indeed use different terms to distinguish between them. For example, Kazaux et al. (2016) acknowledge that: These constraints favour the use of ...
Leo Martins's user avatar
4 votes

How to make a distinction between the "classical" de Bruijn graph and the one described in NGS papers?

In addition to the regular De Bruijn graph as depicted on the wikipedia, some implementations in bioinformatics feature additional processing. I guess the main reason figure 1 in the paper you linked (...
holmrenser's user avatar
4 votes
Accepted

Extract sequence context of high-degree nodes in assembly graphs

I don't have a recommendation of specific tools, but we might be able to use the GFA file itself to get at this with just bash commands. For these examples I use the linked GFA here, which is a ...
Maximilian Press's user avatar
3 votes

Extract sequence context of high-degree nodes in assembly graphs

Edit: I've written a short blog post describing my use of nodeSeqs.sh to investigate the functions of sequences at the nodes of short-read assembly graphs for a set of human oral microbiome samples. ...
acvill's user avatar
  • 613
3 votes

How to make a distinction between the "classical" de Bruijn graph and the one described in NGS papers?

Let's first assume DNA only has one strand. An assembly de Bruijn graph is a subgraph of a complete de Bruijn graph. It contains a vertex u if u is a k-mer in reads; it contains an edge u->v, if u and ...
user172818's user avatar
  • 6,525

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